I think there are several factors that affect this trend:
1. National running trend (defined by number of running event finishers) has been decreasing since 2013.
2. National number of running events has actually increased (at least through 2015 - don't yet have data for 2016).
3. runDisney has added more running events in recent years.
4. runDisney has reduced the unique features of their races (or altogether canceled unique races), so less motivation to attend multiple races in one year.
5. runDisney races are very expensive (not just the entry fee, but the combination of entry fee, hotel, flight, food, car rental, add-on family vacation, etc).
6. Many folks first races were with runDisney (because they were Disney fans before they were runners), and then they either stopped after they checked it off the list, or they liked it and continued (maybe even increased their Disney trips because of the running weekends), but maybe they finally ventured out into the larger running community and found that there are many options for good races (especially local races). Plus, they may want to PR once they get more into it, and rD is not always the best for this (depending on corral placement).
7. runDisney races have huge economic risks for participants: I think Disney has been lucky in the past; however, in just the past few months, we have had a race shortened and a race cancelled (both for good reason). For a local race, it's no big deal if it's changed or cancelled, but this is much different if it's a destination race with huge expense. Also, they have increased economic risk of injury/pregnancy/etc by not allowing for a deferral process. Sure, they graciously provided a refund for the canceled half, but that is minor compared to all the costs associated with the race (for most folks).
Yes, I know runners have similar issues for the NYC, Chicago, Boston, Marine Corps, and LA marathons, but those events are only once per year (where I think Disney has many folks that attended multiple races per year), and those other races are oftentimes one and done (check it off the bucket list). I think rD has a much higher percentage of repeat customers (both for same event year-after-year as well as multiple events in one year), so for each person that decides to stop or reduce their frequency, it affects their overall participant pool greater.